How to send the PDF file with submitted data to a custom server?

2. Are we able to pull these pdf files to our own location for record purposes, like via the API?

You may try integrating your form with Dropbox, Google Drive or sending the submitted data to your own Server, these guides will help you to achieve it.

http://www.jotform.com/help/177-How-to-Enable-FTP-on-Form-Submissions

http://www.jotform.com/help/77-Upload-to-Dropbox-with-JotForm

http://www.jotform.com/help/192-How-to-Integrate-a-Form-with-Google-Drive

 

Thanks for the feedback,